Evidence map›Paper›PMID 38548768›Full record

ArticleNature communications2024

Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL.

Digant Nayak, Dongwen Lv, Yaxia Yuan, Peiyi Zhang, Wanyi Hu, Anindita Nayak, Eliza A Ruben, Zongyang Lv, Patrick Sung, Robert Hromas and 3 more

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.

0numbers the graph read from it
0cells of the map it votes in
30citing papers in PubMed
8.9field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

30 citing papers in PubMed, 38 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors at 2 institutions in 1 country.

Digant Nayak *Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.ORCID http://orcid.org/0000-0003-3680-0846
Dongwen Lv *Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.ORCID http://orcid.org/0000-0003-4677-8996
Yaxia YuanDepartment of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
Peiyi ZhangDepartment of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA.
Wanyi HuDepartment of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA.
Anindita NayakDepartment of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
Eliza A RubenDepartment of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
Zongyang LvDepartment of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
Patrick SungDepartment of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.ORCID http://orcid.org/0000-0003-1396-9040
Robert HromasDepartment of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
Guangrong ZhengDepartment of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA. zhengg@cop.ufl.edu.ORCID http://orcid.org/0000-0002-8106-6663
Daohong ZhouDepartment of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA. zhoud@uthscsa.edu.
Shaun K OlsenDepartment of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA. olsens@uthscsa.edu.ORCID http://orcid.org/0000-0002-1265-7101
The University of Texas Health Science Center at San Antonio · USUniversity of Florida · US

Funding

TISSUE CULTURE---COREP30CA054174 · NCI · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI Robin Jean Leach · 1991 to 2026
$59.1M
User Training and OutreachP30GM124165 · NIGMS · CORNELL UNIVERSITY · PI Nozomi Ando, J Christopher Fromme · 2018 to 2026
$34.2M
TRANSGENIC COREP30AG013319 · NIA · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI JAMES FLOYD NELSON · 1995 to 2026
$30.6M
EEPD1 Repair of Stressed Replication ForksR01CA205224 · NCI · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI Robert A Hromas · 2016 to 2026
$3.3M
Structural Biology of the Ubiquitin Conjugation SystemR01GM115568 · NIGMS · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI OLSEN, SHAUN · 2015 to 2023
$2.7M
Inhibition of Bcl-xL by Targeted DegradationR01CA241191 · NCI · UNIVERSITY OF FLORIDA · PI KONOPLEVA, MARINA Y, ZHENG, GUANGRONG · 2020 to 2024
$2.6M
Use of BCL-xL Proteolysis targeting chimeras to treat pancreatic cancerR01CA242003 · NCI · UNIVERSITY OF FLORIDA · PI TREVINO, JOSE G., ZHENG, GUANGRONG · 2019 to 2023
$2.6M
Develop BCL-xL proteolysis targeting chimeras as safer and better senolyticsR01AG063801 · NIA · UNIVERSITY OF FLORIDA · PI ELISSEEFF, JENNIFER H, ZHENG, GUANGRONG · 2019 to 2023
$2.6M
Structure and Function of the Essential Cell Cycle Regulator Cdc34R01GM128731 · NIGMS · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI Shaun Olsen · 2019 to 2026
$2.5M
Pixel Array Detector for Macromolecular CrystallographyS10OD021527 · OD · CORNELL UNIVERSITY · PI EALICK, STEVEN E · 2016 to 2016
$2.0M
Orbitrap Exploris 480 Mass Spectrometer for Biomedical ResearchS10OD030371 · OD · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI WEINTRAUB, SUSAN T · 2022 to 2022
$882k
Upgrade of a Core Laboratory Macromolecular X-ray Diffraction SystemS10OD030374 · OD · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI TAYLOR, ALEXANDER B · 2021 to 2021
$439k
NCI NIH HHS P30 CA054174NCI NIH HHS R01 CA205224NCI NIH HHS R01 CA241191NCI NIH HHS R01 CA242003NCI NIH HHS R21 CA286307NIA NIH HHS P30 AG013319NIA NIH HHS R01 AG063801NIGMS NIH HHS P30 GM124165NIGMS NIH HHS R01 GM115568NIGMS NIH HHS R01 GM128731NIH HHS S10 OD021527NIH HHS S10 OD030371NIH HHS S10 OD030374
6 · The paper itself

Abstract

Overexpression of BCL-xL and BCL-2 play key roles in tumorigenesis and cancer drug resistance. Advances in PROTAC technology facilitated recent development of the first BCL-xL/BCL-2 dual degrader, 753b, a VHL-based degrader with improved potency and reduced toxicity compared to previous small molecule inhibitors. Here, we determine crystal structures of VHL/753b/BCL-xL and VHL/753b/BCL-2 ternary complexes. The two ternary complexes exhibit markedly different architectures that are accompanied by distinct networks of interactions at the VHL/753b-linker/target interfaces. The importance of these interfacial contacts is validated via functional analysis and informed subsequent rational and structure-guided design focused on the 753b linker and BCL-2/BCL-xL warhead. This results in the design of a degrader, WH244, with enhanced potency to degrade BCL-xL/BCL-2 in cells. Using biophysical assays followed by in cell activities, we are able to explain the enhanced target degradation of BCL-xL/BCL-2 in cells. Most PROTACs are empirically designed and lack structural studies, making it challenging to understand their modes of action and specificity. Our work presents a streamlined approach that combines rational design and structure-based insights backed with cell-based studies to develop effective PROTAC-based cancer therapeutics.

Indexed as

NeoplasmsProto-Oncogene Proteins c-bcl-2bcl-X ProteinHumansbcl-X ProteinProto-Oncogene Proteins c-bcl-2

Identifiers

PMID38548768
PMCPMC10979003
OpenAlexW4393314657

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.